Objects messed up when I re-open the file
Because you have keyframed Location, Rotation and Scale values.
To see the issue you don't have to reopen file, just move on Timeline to another frame.
After Apply Ctrl+A All Transforms you have to set keyframes again I. Yellow color indicates keyframed value, orange edited/unsaved a change.
What is happening here? When you apply transforms they became to zero and  1 for scale, but unsaved keyframes remember saved value and when you move on timeline or reopen file, they &quot;jump&quot; back, so they are used like twice now.